Re: Congruence and phylogenetic reanalysis of perching bird cytochrome b sequences

In a study of the phylogenetic relationships among perching bird mtDNA sequences, Edwards et al. (1991; Proc. R. Soc. London Ser B. 243: 99-107) sequenced part of the mitochondrial cytochrome b gene from 13 perching birds (Passeriformes) and a woodpecker outgroup. However, recently the validity of part of the sequence of the hermit thrush (Catharus guttatus) in that study has been questioned. To determine the effect of inclusion of this apparently chimeric sequence on the conclusions of the original analysis, we reanalyzed these sequences using a different published hermit thrush sequence. In addition, we applied tests of congruence to examine the possibility that the aberrant phylogenetic behavior of chimeric mtDNA sequences might be detected. The reanalysis confirms the ability of slow evolving first and second codon positions of cytochrome b sequences to resolve deep branches in the avian tree. The fact that the new data set does not reject the DNA hybridization tree of these species probably indicates poor ability of the cytochrome b sequences to discriminate among alternative trees, rather than consistency among data sets. Statistical testing of trees based on individual amplified segments of mtDNA indicates that congruence tests may be one useful way of identifying chimeric mtDNA sequences when they have not been detected in the laboratory or during standard phylogenetic analysis.